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Yorodumi- PDB-3o16: Crystal Structure of Bacillus subtilis Thiamin Phosphate Synthase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o16 | ||||||
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Title | Crystal Structure of Bacillus subtilis Thiamin Phosphate Synthase K159A | ||||||
Components | Thiamine-phosphate pyrophosphorylase | ||||||
Keywords | TRANSFERASE / thiamin biosynthesis / TIM barrel | ||||||
Function / homology | Function and homology information thiamine phosphate synthase / thiamine-phosphate diphosphorylase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | McCulloch, K.M. / Hanes, J.W. / Abdelwahed, S. / Mahanta, N. / Hazra, A. / Ishida, K. / Begley, T.P. / Ealick, S.E. | ||||||
Citation | Journal: to be published Title: Crystal Structure and Kinetic Characterization of Bacillus subtilis Thiamin Phosphate Synthase with a Carboxylated Thiazole Phosphate Authors: McCulloch, K.M. / Hanes, J.W. / Abdelwahed, S. / Mahanta, N. / Hazra, A. / Ishida, K. / Begley, T.P. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o16.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o16.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 3o16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/3o16 ftp://data.pdbj.org/pub/pdb/validation_reports/o1/3o16 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25239.650 Da / Num. of mol.: 1 / Mutation: K159A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU38290, ipa-26d, thiC, thiE, ywbK / Plasmid: p28nTEV / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P39594, thiamine phosphate synthase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: 22-28% PEG4000, 75 mM MgCl2, 1 mM DTT, 100 mM Tris, pH 7.7, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 14986 / % possible obs: 91.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Χ2: 1.151 / Net I/σ(I): 13.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→34.63 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 45.6699 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 66.91 Å2 / Biso mean: 34.5178 Å2 / Biso min: 16.41 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→34.63 Å
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Refine LS restraints |
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Xplor file |
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